source: trunk/components/bio-formats/src/loci/formats @ 7043

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Diff Rev Age Author Log Message
(edit) @7043   9 years melissa Fixed stage position indices, see #576.
(edit) @7042   9 years melissa Parse and apply channel colors stored in ND2 files.
(edit) @7041   9 years melissa Added support for pixel types other than uint8.
(edit) @7040   9 years melissa Progress on reading position data from LSM files. See #576, see #570.
(edit) @7039   9 years melissa Several metadata population fixes.
(edit) @7038   9 years melissa Adjusted original metadata population, so that it doesn't take nearly as …
(edit) @7037   9 years melissa One more very temporary fix that prevents too many Channels from being …
(edit) @7022   9 years melissa Fixed a few little bugs that prevented tests from passing in r7021.
(edit) @7021   9 years melissa Updated FileStitcher and FilePattern to better handle multi-series …
(edit) @7019   9 years melissa Added support for RGB and indexed color images. Closes #567.
(edit) @7010   9 years melissa Fixed a bug that prevented extra LIF channels from being removed. Closes …
(edit) @7009   9 years melissa Fixed SVN/Trac links.
(edit) @6988   9 years melissa Fixed a couple of issues exposed by Findbugs. See #546.
(edit) @6987   9 years melissa Parse scanner serial numbers from the plate log file.
(edit) @6986   9 years melissa Minor fixes to (hopefully) prevent AIOOB.
(edit) @6983   9 years melissa Fixed various dimension ordering bugs in new multi-file Improvision TIFF …
(edit) @6981   9 years melissa Only populate a channel's excitation wavelength if the wavelength is …
(edit) @6978   9 years melissa OMETiffReader now populates its' MetadataStore in such as way as to …
(edit) @6977   9 years melissa Fixed TiffParser constructor, so that it effectively does not modify the …
(edit) @6976   9 years melissa Several fixes for writing BigTIFFs and multi-series OME-TIFFs. Closes …
(edit) @6975   9 years melissa One more set of ArrayIndexOutOfBounds fixes for certain LZW-compressed …
(edit) @6970   9 years melissa Support for multi-file Improvision/Volocity TIFF datasets.
(edit) @6969   9 years melissa Scan TiffData elements for 1-indexed indices before assembling list of …
(edit) @6968   9 years melissa Prevent ArrayIndexOutOfBoundsException when decompressing certain …
(edit) @6967   9 years melissa Fixed SizeT calculation.
(edit) @6965   9 years melissa Tweaked field index calculation.
(edit) @6959   9 years melissa Fixed well dimension parsing and calculation, so that the ScanR reader no …
(edit) @6958   9 years melissa Fixed error in plane index calculation.
(edit) @6953   9 years melissa Allow MIAS text files to be passed to MIASReader.setId. Closes #562.
(edit) @6952   9 years melissa Prevent Image names from being overwritten. Closes #555.
(edit) @6945   9 years melissa Parse 'waitTime' from Prairie datasets. Closes #551.
(edit) @6917   9 years callan Solution for underscores in wavelength names. (Fixes #558)
(edit) @6890   9 years melissa A few fixes for ScanR datasets with missing wells, based on a patch …
(edit) @6886   9 years melissa * Improved metadata parsing for Prairie datasets. * Reverted changes to …
(edit) @6881   9 years curtis Update SVN and Trac paths.
(edit) @6880   9 years melissa Couple of findbugs fixes, see #546.
(edit) @6878   9 years melissa Fixed bugs in writing and reading JPEG- and JPEG-2000-compressed TIFFs. …
(edit) @6877   9 years melissa * Return blank planes if pixel data is missing from an OME-XML file. * …
(edit) @6876   9 years callan Some further test case cleanup. Added a check to ChannelFiller to handle …
(edit) @6875   9 years melissa Fixed handling of multi-position ND2 datasets.
(edit) @6872   9 years melissa Fixed OMETiffWriter.close() so that it releases resources even if an …
(edit) @6866   9 years melissa Removed support for JPEG/JPEG-2000 compression in OME-XML files, as this …
(edit) @6864   9 years melissa Several tweaks to original metadata storage so that FV1000 files do not …
(edit) @6863   9 years melissa Added missing methods that prevented r6862 from compiling.
(edit) @6862   9 years melissa Simplified search for BinData offsets.
(edit) @6861   9 years callan Reverting erroneous debugging in OMEXMLReader from r6860.
(edit) @6860   9 years callan Added a test case (and re-organized some of the mock infrastructure) for …
(edit) @6857   9 years melissa Added support for multi-chunk AVI files.
(edit) @6856   9 years melissa Fixed sub-image reading for SimplePCI files that contain embedded TIFFs.
(edit) @6854   9 years curtis Use INFO logging for AxisGuesser main.
(edit) @6853   9 years curtis Use INFO logging in FilePattern main.
(edit) @6852   9 years melissa Prevent a bunch of NPEs.
(edit) @6845   9 years melissa Added support for Varian FDF files. Closes #474.
(edit) @6844   9 years melissa Sped up original metadata hashtable population.
(edit) @6843   9 years melissa Removed check that prevented multi-file OME-TIFF export from working.
(edit) @6842   9 years melissa Added support for multi-position Zeiss LSM data. Closes #527.
(edit) @6841   9 years melissa * Updated MetadataConverter to properly handle LightSource attributes. * …
(edit) @6840   9 years callan Support for type resolution of light sources. Re-run of code generation. …
(edit) @6838   9 years melissa One more signedness fix, as pointed out by Rubén Muñoz.
(edit) @6836   9 years melissa Fixed Image indexed passed to …
(edit) @6835   9 years melissa A few changes to how pixels and dimension information are found. I'm not …
(edit) @6834   9 years melissa Moved MetadataStore calls that depend on MetadataTools.populatePixels(...) …
(edit) @6823   9 years melissa Added reader for TIFFs produced by Nikon Elements. Closes #529.
(edit) @6822   9 years melissa Prevent extra (Logical)Channel objects from being populated.
(edit) @6819   9 years melissa Factored ND2Handler out of NativeND2Reader. See #529.
(edit) @6816   9 years melissa Fixed hack from r6804 so that it won't throw an AIOOB exception.
(edit) @6814   9 years melissa Reverted a few changes from r6791 that prevented OME-TIFF files from being …
(edit) @6812   9 years melissa Reverse the order of the rows if a negative height was stored in the file. …
(edit) @6810   9 years melissa Force the pixel type to be unsigned, regardless of what is actually stored …
(edit) @6808   9 years melissa If a negative width or height is stored, use the absolute value instead …
(edit) @6805   9 years melissa * Added convenience method to loci.common.IniList to flatten the IniTables …
(edit) @6804   9 years melissa Hackish fix for some files that have an incorrect dimension order.
(edit) @6802   9 years melissa * Ignore missing L2D scans, instead of throwing an exception. * More …
(edit) @6801   9 years melissa * Parse metadata from SimplePCI TIFFs. * Slightly better Z/T detection for …
(edit) @6800   9 years melissa Remove invalid characters from strings that will later be parsed into …
(edit) @6799   9 years melissa Fixed a few Bio-Rad Gel offset bugs.
(edit) @6798   9 years melissa Added 'Object getSeriesMetadataValue(String)' to IFormatReader.
(edit) @6797   9 years melissa Added support for FEI TIFF files, specifically those from S-FEG and Helios …
(edit) @6796   9 years melissa Remainder of OME-XML validation fixes. Closes #520.
(edit) @6791   9 years melissa More OME-XML validation fixes, see #520.
(edit) @6790   9 years melissa Initial version of ECAT 7 reader. Closes #487.
(edit) @6789   9 years curtis Fix for NullPointerException.
(edit) @6787   9 years melissa Added extra sanity check when parsing doubles.
(edit) @6786   9 years melissa More OME-XML validation fixes, see #520.
(edit) @6785   9 years melissa * bfconvert and showinf now exit if an unknown flag or argument is …
(edit) @6784   9 years melissa More OME-XML validation fixes. See #520.
(edit) @6783   9 years melissa Removed not-yet-existent CRIReader.
(edit) @6782   9 years melissa Parse physical pixel sizes for all series, instead of applying the first …
(edit) @6781   9 years melissa Fixed tests in components/bio-formats; all tests should now pass.
(edit) @6780   9 years melissa More thoroughly parse Z position values from single-file datasets.
(edit) @6779   9 years melissa Fixed tag alignment problem.
(edit) @6778   9 years melissa Prevent SlidebookReader from passing a negative int to setSeries.
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